On Sat, May 18, 2013 at 5:17 PM, bharat gupta <bharat.85.m...@gmail.com>wrote:
> Dear Sir, > > My main objective of carrying out REMD is to study peptide folding and if > possible to get some insight in protein design and folding. I read some > articles related to my work and they always show temp (replica_index) > graphs for 2-3 replicas , saying that the sufficient sampling had been > achieved. In my case I checked the replica_temp for first three replicas ( > https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png) ( > https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png) > https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png) > You've shown the same graph three times. > Almost all the three graphs are similar and the last 15ns shows that there > is no enough exchange (if I have analyzed correctly) ?? In this case the > acceptance ratio was fine and PE overlap was also good, but problem lies > with efficient sampling ?? Like I've been saying, acceptance does not assure enhanced sampling. > What shall I do in such a case ?? > Do some of the reading I've been suggesting? One of the papers shows that it is hard to get good sampling with just Met-enkephalin unless you design the temperature range for it. Mark On Sat, May 18, 2013 at 12:27 AM, Mark Abraham <mark.j.abra...@gmail.com > >wrote: > > > On Fri, May 17, 2013 at 4:26 PM, bharat gupta <bharat.85.m...@gmail.com > > >wrote: > > > > > Dear Sir, > > > > > > The the default bin width is 0.1 which I used for plotting the graphs. > > > > > > > That's nice. You need to decide what you need to do about it if you want > > graphs that look like those you see reported :-) > > > > > > > Another question is about your last reply to my thread "exchange > > acceptance > > > is a poor proxy for sampling efficiency". Sorry to ask this, but how to > > > check whether the sampling efficiency is optimal or not (what should be > > > optimal sampling efficiency) ?? > > > > > > > Ah, now here's the real question :-) Spacing the replicas for optimal > > *flow* is a difficult problem, even for toy peptides, see e.g. papers by > > Nadler and Hansmann. Merely accepting exchanges does not imply flow. The > > belief is that getting flow enhances sampling, but the latter is hard to > > demonstrate without showing that "simulation time to converged sampling" > > actually reduces. I'm not aware of anybody who's actually done that - but > > it would certainly be an advantage if your application is interested in > > data at a range of temperatures. > > > > Mark > > > > On Fri, May 17, 2013 at 11:10 PM, Mark Abraham <mark.j.abra...@gmail.com > > > >wrote: > > > > > > > Histograms 101: The smaller your bin width, the more variations you > > see. > > > > The more samples you have, the fewer variations you see. A histogram > > that > > > > does not mention either of this is a work of fiction. > > > > > > > > The number of degrees of freedom in the potential energy distribution > > is > > > > also a factor in whether the distribution will look smooth for a > given > > > bin > > > > width and number of samples. > > > > > > > > Mark > > > > > > > > On Fri, May 17, 2013 at 3:51 PM, bharat gupta < > > bharat.85.m...@gmail.com > > > > >wrote: > > > > > > > > > Dear Sir, > > > > > > > > > > I tried plotting the PE overlap using the following way :- > > > > > > > > > > 1. extract PE of each replica using g_energy > > > > > 2. get the PE distribution using g_analyze -f potential_0.xvg -dist > > > > > pot0.xvg > > > > > 3. used xmgrace to plot all the PE distribution graphs together. > > > > > > > > > > The same thing I did for temperature distribution for each replica. > > > > > > > > > > Here's the file for both PE overlap ( > > > > > https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) > > > > > temp distribution ( > > > > https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png > > > > > ) > > > > > Is this the correct way ?? > > > > > > > > > > > > > > > But the plot doesnot look like this ( > > > > > > https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg > > ). > > > > Do i > > > > > have to normalize the data and then plot in order to get a smooth > > plot > > > > like > > > > > this one?? > > > > > > > > > > -------- > > > > > Bharat > > > > > -- > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > -- > > > > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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